Open research questions in Genomic variations and chromosomal abnormalities
164 gap statements mined from Genomic variations and chromosomal abnormalities papers in our 7.9M-paper local library, which holds 821 papers on the topic — drawn mostly from each paper's own stated research gap, future-work, challenge and limitation notes, and its abstract. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one.
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What the literature leaves open
Limited understanding of the molecular mechanisms underlying PMS. Technical challenges in detecting microdeletions and pathogenic variants in SHANK3.
Prenatal and Postnatal Identification of Phelan–McDermid Syndrome in a Tertiary Referral Center: A 15-Case Series and Literature Review · 2026 · DOIHowever, the contributions of ring chromosome instability, tissue-specific mosaicism, and complex dosage imbalance to the clinical phenotype remain poorly understood.
Dynamic tissue-specific mosaicism in constitutional non-supernumerary ring chromosome 21 with a Down syndrome-like phenotype: a case report and genotype-phenotype analysis · 2026 · DOIWhile deletions of chromosome 19 have been associated with various clinical conditions, duplications remain poorly characterised.
However, the association of interstitial deletions in chromosome 10q with global developmental delay, musculoskeletal abnormalities, and dysmorphic features has not been previously reported.
Neurodevelopmental delay, musculoskeletal disorders and dysmorphia associated with a novel pathogenic interstitial deletion of chromosome 10q21.1q21.3 · 2025 · DOIA promising approach to solving such challenging cases arises with access to optical genome mapping (OGM) but has not been systematically explored as of yet.
Retrospective study on the utility of optical genome mapping as a follow-up method in genetic diagnostics · 2024 · DOIHowever, little is known about inflammation and its relationship to clinical phenotypes in 22q11.
Differential inflammatory profiles in carriers of reciprocal 22q11.2 copy number variants · 2024 · DOIThe lack of understanding of the genetic mechanisms underlying the neurodevelopmental phenotype. The limited number of prenatal cases reported in the literature.
SRSF1 haploinsufficiency drives the neurodevelopmental phenotype of the 17q22 deletion syndrome · 2026 · DOIThe joint contributions of rare and common genetic variation, development, and environment to complex traits are not well understood. Prior studies have been limited by statistical power. There is a need for a standardized pipeline for CNV genotype assignment.
Combinatorial effects of gene dosage, polygenic background and environment on complex traits · 2026 · DOIThe need for a deeper understanding of the etiology and pathogenesis of hereditary diseases. The need for effective prenatal screening and genetic counseling.
Future work will focus on stain normalization, upstream instance segmentation to further mitigate borderline overlaps, explicit probability calibration, band-aware representations for acrocentric discrimination, and multi-center validation to assess robustness under heterogeneous imaging conditions.
Automated karyotyping and structural anomaly detection through a hybrid multi-stage deep learning framework integrating chromosome detection, pairwise classification, and autoencoder-based analysis · 2026 · DOIThe impact of reversion on aneuploid karyotype stability and persistence in populations is unclear. The mechanisms underlying aneuploid karyotype dynamics are not well understood.
Future research should investigate the mechanisms underlying the development of multiple organ dysfunction syndrome in patients with Turner syndrome. Future research should explore the effectiveness of different treatment strategies in patients with Turner syndrome and multiple organ dysfunction syndrome.
Case Report: Infection-triggered multiple organ dysfunction syndrome as the initial presentation of undiagnosed turner syndrome in an 11-Year-Old girl · 2026 · DOIThere is a lack of understanding of the potential for Turner syndrome to present as acute, life-threatening multiple organ dysfunction syndrome in children. There is a need for early genetic diagnosis and multidisciplinary management in patients with Turner syndrome and multiple organ dysfunction syndrome.
Case Report: Infection-triggered multiple organ dysfunction syndrome as the initial presentation of undiagnosed turner syndrome in an 11-Year-Old girl · 2026 · DOIThe molecular mechanisms underlying complex chromosomal rearrangements are not well understood. Long-read sequencing can be used to fill this gap. The study aims to provide a better understanding of the mechanisms underlying complex chromosomal rearrangements.
Long-read genome sequencing resolves a de novo complex 18q12.1q21.2 triplication causing partial tetrasomy and reveals its underlying mechanism · 2026 · DOIThe roles of transposable elements in the human brain remain largely unresolved. Short-read sequencing lacks the resolution to accurately map TE insertions.
Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain · 2026 · DOIFurther studies are needed to investigate the clinical significance of the genotypes in the study population. The HRM assay should be validated in larger and more diverse populations. The study's findings can inform the development of personalized medicine approaches for UGT1A1-related disorders.
Analytical validation of a high-resolution melting assay for UGT1A1 TATA-box polymorphisms · 2026 · DOIAnother challenge is the need for comprehensive pathogenicity assessment of these variants. The study also highlights the challenge of understanding the molecular mechanisms underlying the disease spectrum of PAPSS2 deficiency.
Reclassification of PAPSS2 Missense Variants in Turkish Patients with Brachyolmia Type 4: Multi-Modal Computational and Structural Biology Evidence for APS-Kinase Domain Dysfunction · 2026 · DOIThe molecular association between CPAM IV and early-stage PPB is not well understood. There is a need to identify the genetic variants associated with CPAM IV. The relationship between CPAM IV and PPB is controversial.
Case Report: Congenital pulmonary airway malformation associated with a germline DICER1 splicing variant · 2026 · DOIIn-depth study of the topic will contribute significantly to the advancement of medical genetics and reproductive medicine. Technologies such as CRISPR gene editing, folate supplementation, and control of age-related risks can substantially reduce disease incidence.
The sample size was limited to 106 samples. The study did not investigate the clinical significance of the genotypes in the study population.
Analytical validation of a high-resolution melting assay for UGT1A1 TATA-box polymorphisms · 2026 · DOIThe paper identifies a gap in the understanding of human genetics and its role in medicine. The paper identifies a gap in the understanding of the cytogenetic method and its importance in detecting genetic diseases.
Not all findings underwent confirmatory evaluation due to factors including loss to follow-up, insurance limitations, clinical circumstances, or provider preference - The study was retrospective - The study had a limited sample size of 679…
Chromosomal Microarray Analysis in Critically Ill Neonates and Children: Diagnostic Yield and Clinical Utility · 2026 · DOIFurther studies are needed to evaluate the long-term outcomes of patients with clinically relevant CNVs - Research is needed to determine the clinical utility of CMA in different patient populations - Studies should investigate the impact of CMA on healthcare utilization and clinical…
Chromosomal Microarray Analysis in Critically Ill Neonates and Children: Diagnostic Yield and Clinical Utility · 2026 · DOIHi-C has limited resolution - ChIP-Seq requires specific, high-quality antibodies and samples - CUT&RUN has yet to be standardized for clinical…
Development of spatial transcriptomics and transcriptome-wide association studies (TWAS) - Development of single-cell CUT&RUN and other single-cell assays - Use of CRISPR/Cas-based therapies to treat genetic and genomic…
Most-cited papers in Genomic variations and chromosomal abnormalities
- A second generation human haplotype map of over 3.1 million SNPs · Nature · 2007 · 3,825 citations
- Global variation in copy number in the human genome · Nature · 2006 · 3,436 citations
- Identification of the Cystic Fibrosis Gene: Chromosome Walking and Jumping · Science · 1989 · 2,434 citations
- Strong Association of De Novo Copy Number Mutations with Autism · Science · 2007 · 2,327 citations
- A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms · Nature · 2001 · 2,264 citations
- A Single Ataxia Telangiectasia Gene with a Product Similar to PI-3 Kinase · Science · 1995 · 2,205 citations
- Genetic Dissection of Complex Traits · Science · 1994 · 2,145 citations
- A comprehensive genetic map of the human genome based on 5,264 microsatellites · Nature · 1996 · 2,103 citations
- Large-Scale Copy Number Polymorphism in the Human Genome · Science · 2004 · 1,983 citations
- A draft human pangenome reference · Nature · 2023 · 1,170 citations
Most recent work
- Advancing regulatory variant effect prediction with AlphaGenome · Nature · 2026
- A Beginner's Guide to Structural Variants in Eco‐Evolutionary Population Genomics · Molecular Ecology · 2026
- A complete diploid human genome benchmark for personalized genomics · Cell · 2026
- Genetic drivers and clinical consequences of mosaic chromosomal alterations in 1 million individuals · medRxiv · 2026
- A breakage–replication/fusion process explains complex rearrangements and segmental DNA amplification · Nature Genetics · 2026
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation · bioRxiv · 2026
- Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases · The American Journal of Human Genetics · 2026
- Patterns and drivers of 43,617 mosaic chromosomal alterations in blood · Nature Genetics · 2026
- Points to consider for the next-generation-sequencing-based detection of copy-number abnormalities (CNAs) and balanced chromosomal rearrangements in neoplastic disorders: A statement of the American College of Medical Genetics and Genomics (ACMG) · Genetics in Medicine · 2026
- Rare and Common Genomic Copy Number Variants Associated with Strabismus and Amblyopia in the All of Us Research Program · medRxiv · 2026
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